Reaction–Diffusion Patterning of DNA-Based Artificial Cells

Abstract

Biological cells display complex internal architectures with distinct micro environments that establish the chemical heterogeneity needed to sustain cellular functions. The continued efforts to create advanced cell mimics, namely, artificial cells, demands strategies for constructing similarly heterogeneous structures with localized functionalities. Here, we introduce a platform for constructing membraneless artificial cells from the self-assembly of synthetic DNA nanostructures in which internal domains can be established thanks to prescribed reaction–diffusion waves. The method, rationalized through numerical modeling, enables the formation of up to five distinct concentric environments in which functional moieties can be localized. As a proof-of-concept, we apply this platform to build DNA-based artificial cells in which a prototypical nucleus synthesizes fluorescent RNA aptamers that then accumulate in a surrounding storage shell, thus demonstrating the spatial segregation of functionalities reminiscent of that observed in biological cells.

A synthetic signalling network imitating the action of immune cells in response to bacterial metabolism

“…The amphiphilic core motifs (CM) consist of 4-pointed DNA junctions (nanostars), with the end of each double-stranded (ds) DNA arm labelled by a cholesterol moiety. Similar “C-star” designs have been shown to self-assemble into framework-like materials sustained by cholesterol-mediated hydrophobic forces, with programmable nanoscale morphology and multi-stimuli-responsiveness [27, 54, 61–63]. The shell comprises of two 6-pointed all-DNA nanostars, labelled as inner and outer corona motifs (ICM and OCM, respectively), together forming dendrimeric construct that can connect to core motifs through single-stranded (ss) DNA overhangs (Fig.…”

“…This interest has led to a rapid expansion of the available design toolkit for artificial cells, enabling replication of biological processes and features such as division [14–16], metabolism [17, 18], growth [19], motility [20, 21], communication [22, 23], sensing [24, 25], compartmentalisation [26–28], protein expression [29] and DNA replication [30]. Artificial cells have been successfully built from membrane-bound scaffolds in the form of liposomes [31, 32], polymer-somes [31, 33] and proteinosomes [34, 35], as well as from membrane-less coacervates or hydrogels [27, 36–39].…”

DNA Droplets: Intelligent, Dynamic Fluid

“…), as will be explained in detail below. Thus, the multi-branch motifs provide scientists and engineers with a robust and facile route toward well-engineered hierarchical droplet architectures [11,16,19,20] and flexibility-controlled phase behavior. [18,25] In addition to the motif-based fabrication, other methods are available for the fabrication of DNA droplets.…”

“…Very recently, reaction–diffusion waves were generated within a spherical geometry of DNA droplets. [ 20 ] In the presence of free ssDNAs of varied length outside the droplets, the strands diffused into the droplets at different paces, determined by the length‐dependent diffusion coefficients. As a result, waves of strand displacement reactions propagated in a radial direction in the droplets, generating the reaction–diffusion patterns.…”

“…[9,10] In the context of artificial cell studies, DNA droplets have emerged as a promising biomaterial for the construction of intelligent artificial cells (Figure 1A). [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] DNA droplets are micrometer-scale liquid-like condensate composed purely, or at least mostly, of DNA, a biomolecule in which genetic information is encoded. Since the first report published in 2018, [14] several groups have explored DNA droplets to demonstrate their fundamental functions, properties, and advantages, which are not parallel to other biomolecules.…”